RetrogeneDB ID:

retro_mmul_358

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:1:22257962..22258272(+)
Located in intron of:ENSMMUG00000005855
Retrocopy
information
Ensembl ID:ENSMMUG00000003234
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.4224
Ensembl ID:ENSMMUG00000002848
Aliases:None
Description:40S ribosomal protein S14 [Source:RefSeq peptide;Acc:NP_001253845]


Retrocopy-Parental alignment summary:






>retro_mmul_358
GATGAAGGGGAAAGCAGACCGAGATGAATCCTTGCTATGTTGGCCACCCAGGATGTGGCCCAGAGGTGCAAGGAGCTGGG
TATCATTGCCCTACACATCCAACTCCGAGCCACAGGAGGAAATAGGACCAAGACCCTTGGACCTGGGGCCCAGTTGGCCC
TCAGAGCCCTTGTCTGCTCTGGTATGAAGATCAGGAGAATTGAGGACGCCACCCCCATCCCCTCTGACAGCACTCACAGG
AATGGGGGTTGCCGTGGTCGCCGTCTGTGAACAAGACTCCTCAAAATATTTTCTGTTAATAAATTGCCTT

ORF - retro_mmul_358 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.92 %
Parental protein coverage: 59.17 %
Number of stop codons detected: 1
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalDRDESSP--YAAMLAAQDVAQRCKELGITALHIKLRATGGNRTKTPGPGAQSALRALARSGMKIGRIEDV
D..ES.P....AMLA.QDVAQRCKELGI.ALHI.LRATGGNRTKT.GPGAQ.ALRAL..SGMKI.RIED.
RetrocopyDEGESRPR*ILAMLATQDVAQRCKELGIIALHIQLRATGGNRTKTLGPGAQLALRALVCSGMKIRRIEDA
ParentalT-PIPSDS-TRRGVAVVAVCEQDSSKYFLLINCL
T.P.P....T..GVAVVAVCEQDSSKYFLLINCL
RetrocopyT>PSPLTALTGMGVAVVAVCEQDSSKYFLLINCL

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain 0 .11 RPM 100 .62 RPM
SRP007412_brain_prefrontal_cortex 0 .08 RPM 190 .07 RPM
SRP007412_cerebellum 0 .19 RPM 110 .29 RPM
SRP007412_heart 0 .12 RPM 250 .20 RPM
SRP007412_kidney 0 .35 RPM 237 .32 RPM
SRP007412_liver 0 .04 RPM 341 .77 RPM
SRP007412_testis 0 .04 RPM 157 .67 RPM

ChIP-Seq - click to see more details

Macaca mulatta was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mmul_358 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_358 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_358 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_119
Pan troglodytes retro_ptro_130
Gorilla gorilla retro_ggor_222
Pongo abelii retro_pabe_494
Parental genes homology:
Parental genes homology involve 34 parental genes, and 130 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000150041 retrocopy
retro_acar_201,
Ailuropoda melanoleuca ENSAMEG000000046442 retrocopies
retro_amel_1390, retro_amel_524,
Bos taurus ENSBTAG000000085702 retrocopies
retro_btau_1109, retro_btau_213,
Canis familiaris ENSCAFG000000180942 retrocopies
retro_cfam_1589, retro_cfam_301,
Callithrix jacchus ENSCJAG000000209811 retrocopy
retro_cjac_89,
Cavia porcellus ENSCPOG000000244082 retrocopies
retro_cpor_253, retro_cpor_284,
Dipodomys ordii ENSDORG000000071462 retrocopies
retro_dord_174, retro_dord_330,
Equus caballus ENSECAG000000243363 retrocopies
retro_ecab_127, retro_ecab_282, retro_ecab_522,
Erinaceus europaeus ENSEEUG000000104623 retrocopies
retro_eeur_330, retro_eeur_423, retro_eeur_617,
Echinops telfairi ENSETEG000000028996 retrocopies
retro_etel_1270, retro_etel_1358, retro_etel_1851, retro_etel_1995, retro_etel_293, retro_etel_967,
Felis catus ENSFCAG000000110855 retrocopies
retro_fcat_1140, retro_fcat_622, retro_fcat_670, retro_fcat_857, retro_fcat_925,
Homo sapiens ENSG000001645878 retrocopies
retro_hsap_119, retro_hsap_1622, retro_hsap_268, retro_hsap_3001, retro_hsap_3113, retro_hsap_3232, retro_hsap_3495, retro_hsap_3789,
Gorilla gorilla ENSGGOG000000245938 retrocopies
retro_ggor_1225, retro_ggor_2080, retro_ggor_2135, retro_ggor_2199, retro_ggor_222, retro_ggor_2362, retro_ggor_2548, retro_ggor_316,
Latimeria chalumnae ENSLACG000000161641 retrocopy
retro_lcha_12,
Loxodonta africana ENSLAFG000000311952 retrocopies
retro_lafr_235, retro_lafr_67,
Macropus eugenii ENSMEUG000000149071 retrocopy
retro_meug_619,
Microcebus murinus ENSMICG000000029002 retrocopies
retro_mmur_1569, retro_mmur_433,
Myotis lucifugus ENSMLUG000000132794 retrocopies
retro_mluc_1837, retro_mluc_205, retro_mluc_2464, retro_mluc_2485,
Macaca mulatta ENSMMUG00000002848 5 retrocopies
retro_mmul_1921, retro_mmul_1983, retro_mmul_358 , retro_mmul_570, retro_mmul_90,
Mustela putorius furoENSMPUG000000137761 retrocopy
retro_mputfur_127,
Mus musculus ENSMUSG000000246085 retrocopies
retro_mmus_1362, retro_mmus_1924, retro_mmus_2178, retro_mmus_2252, retro_mmus_2380,
Nomascus leucogenys ENSNLEG000000103661 retrocopy
retro_nleu_101,
Oryctolagus cuniculus ENSOCUG000000115091 retrocopy
retro_ocun_128,
Otolemur garnettii ENSOGAG000000007211 retrocopy
retro_ogar_286,
Ochotona princeps ENSOPRG0000000842217 retrocopies
retro_opri_1012, retro_opri_1074, retro_opri_114, retro_opri_194, retro_opri_258, retro_opri_268, retro_opri_28, retro_opri_306, retro_opri_376, retro_opri_428, retro_opri_707, retro_opri_825, retro_opri_842, retro_opri_876, retro_opri_882, retro_opri_919, retro_opri_971,
Procavia capensis ENSPCAG000000159603 retrocopies
retro_pcap_198, retro_pcap_443, retro_pcap_73,
Pongo abelii ENSPPYG000000159507 retrocopies
retro_pabe_1340, retro_pabe_2487, retro_pabe_2571, retro_pabe_2888, retro_pabe_3204, retro_pabe_401, retro_pabe_494,
Pelodiscus sinensis ENSPSIG000000059221 retrocopy
retro_psin_33,
Pan troglodytes ENSPTRG000000174188 retrocopies
retro_ptro_1086, retro_ptro_130, retro_ptro_2030, retro_ptro_2104, retro_ptro_2184, retro_ptro_224, retro_ptro_2367, retro_ptro_2570,
Rattus norvegicus ENSRNOG0000001877410 retrocopies
retro_rnor_1313, retro_rnor_1467, retro_rnor_1532, retro_rnor_1759, retro_rnor_1875, retro_rnor_1918, retro_rnor_2181, retro_rnor_228, retro_rnor_2728, retro_rnor_873,
Sorex araneus ENSSARG000000142491 retrocopy
retro_sara_537,
Sarcophilus harrisii ENSSHAG000000180523 retrocopies
retro_shar_380, retro_shar_381, retro_shar_503,
Tupaia belangeri ENSTBEG0000000636810 retrocopies
retro_tbel_1147, retro_tbel_1332, retro_tbel_1603, retro_tbel_1868, retro_tbel_202, retro_tbel_3517, retro_tbel_3619, retro_tbel_416, retro_tbel_519, retro_tbel_740,
Tursiops truncatus ENSTTRG000000130351 retrocopy
retro_ttru_566,


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